ASPRAlign: a tool for the alignment of RNA secondary structures with arbitrary pseudoknots

Summary Current methods for comparing RNA secondary structures are based on tree representations and exploit edit distance or alignment algorithms. Most of them can only process structures without pseudoknots. To overcome this limitation, we introduce ASPRAlign, a Java tool that aligns particular algebraic tree representations of RNA. These trees neglect the primary sequence and can handle structures with arbitrary pseudoknots. A measure of comparison, called ASPRA distance, is computed with a worst-case time complexity of (n2) where n is the number of nucleotides of the longer structure. Availability and implementation ASPRAlign is implemented in Java and source code is released under the GNU GPLv3 license. Code and documentation are freely available at https://github.com/bdslab/aspralign. Contact luca.tesei@unicam.it Supplementary information Supplementary data are available at Bioinformatics online.